runTest.yml

name: runTest

on: [push]

jobs:
  test-python-app:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}
    steps:
    - uses: actions/checkout@v2
    - uses: conda-incubator/setup-miniconda@v2
      with:
        activate-environment: yacht
        environment-file: env/yacht_env.yaml
        python-version: 3.11.4
        auto-activate-base: false
        auto-update-conda: true
    - run: |
        conda info
        conda list
        printenv | sort
    - name: make training data
      run: python make_training_data_from_sketches.py --ref_file 'tests/testdata/20_genomes_sketches.zip' --ksize 31 --out_prefix 'gtdb_ani_thresh_0.95' --ani_thresh 0.95                                
    - name: run YACHT
      run: python run_YACHT.py --ref_matrix 'gtdb_ani_thresh_0.95_ref_matrix_processed.npz' --ksize 31 --sample_file 'tests/testdata/sample.sig' --ani_thresh 0.95 --significance 0.99 --min_coverage 1 --outfile 'yacht_results.csv'